Here is a little misunderstanding. As we were not uploading file from the wp-docs so we weren’t editing and/or deleting the files from here. You were being redirected to the library page, there you could edit or delete the files with responsibility.
Library files can be used in multiple posts and pages, so alone wp-docs settings page should not take the decision of removing files from disk.
But, in upcoming version i am removing the file entry from wp-docs in fact. Instead of removing me the file from library, i am just clearing it from current directory. So misunderstanding is clear now.